This paper describes three new taxa of fossil aquatic fungi preserved in 400-million-year-old Lower Devonian Rhynie Chert. All of the fungal morphotypes are attached to cells of the green alga Palaeonitella cranii. Milleromyces rhyniensis is characterized by a holocarpic, epibiotic ^oosporangium with an elongate discharge tube that penetrates the host cell wall; arising from the base of the sporangium is an extensive rhizoidal system. Stages in infection by presumed zoospores are documented. In Lyonomyces pyriformis the globose-pyriform thallus is embedded in the surface coating of the cell wall. At the base of each thallus is a single rhizoid. Krispiromyces is extramatrical, holocarpic, and characterized by a short beak-like discharge papilla. The rhizoidal system appears to be apophysate. Some of these fungi were probably saprobes, while others were deemed parasitic because of the extensive hypertrophy of some of the algal cells. Although not all life history stages are represented, the discovery of these Lower Devonian forms greatly expands our knowledge of the biology and diversity of aquatic fungi in an ancient freshwater ecosystem.